NAME

Opal - system for molecular modelling

DESCRIPTION

Opal is a still-growing system for molecular modelling. It implements the Amber 4.1 potential energy funciton (aka force field) and it is compatbile with Amber's *.top files (describes the structure of the molecule) and *.crd files (contains the three-dimensional coordinates of molecule's atoms).

Why Opal?

It is written in C.: It can be easily modified.
It is free.: You can modify it and distribute it under the terms of GPL (see the section Copyright near the end of this file.
It is portable.: Opal has been tested on different platforms, including the 64-bit ones. It has pain-less configuration via the configure script (generated by the autoconf(1)).
It is fast.: Is it really fast?

Running Opal

There is no program named opal in the Opal system. Instead of this, Opal consists of independent programs - for single-point computations, local and global minimization and a few other utilities. You can use these programs directly or write your own front-end (usually by modifying the main() function of one of the Opal's programs). For information on the Opal internals (data structures and subroutines) see opal_internals(3).

The utilities Opal consists of are:

singlept

This program can evaluate the potential energy for the molecule and the given coordinates as well as the gradient of the force field in this point of the potential hypersurface. It has several levels of verbosity and it can print the energy of each interaction the force field consists of. See opal_singlept(1) for details.

singlept_t

This program is similar to previous. The difference is it can compute the transformed (smoothed) value of the potential energy function. To use this program you must pre-compute the tables describing the transformed function using ??? first. See singlept_t for details.

lmin

Local minimization program. This program can find the local minimum of the potential energy function corresponding to a given start coordinates. It can use the explicit or numerically-computed gradient. See lmin for details.

lmin_t

COPYRIGHT

Opal itself is an open source(tm) software. It can be freely distributed and used under the terms of GNU General Public License. The minimization procedures distributed with Opal in directories vmlm and blas are not freely usable. See their license files for more information.

AUTHORS

Opal was created as part of master thesis of Jan ``Yenya'' Kasprzak, who is the current maintainer of Opal. Some parts of Opal (most notably the lmin program and the function for numerical computing of the gradient) as well as many bug-fixes and suggestions for improvement were contributed by Petr Mejzlík.

BUGS

There are definitively bugs in Opal. The $(STABLE_PROGS) (see the Makefile) should be more stable and bug-free. Send the bugfixes (prefered form is a diff -u output) and bug-reports to Jan ``Yenya'' Kasprzak (kas@fi.muni.cz).